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%\lstinputlisting{nom.txt}
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\section{Exemple de fichiers de METATOOL}
\subsection{Fichier.dat}

\begin{framed}
	\begin{lstlisting}
-ENZREV
Eno Acn SucCD Sdh Fum Mdh AspC Gdh IlvEAvtA

-ENZIRREV
Pyk AceEF GltA Icd SucAB Icl Mas AspCon AspA Pck Ppc Pps GluConAlaCon SucCoACon

-METINT
Ala Asp Glu Gly Mal Fum Succ SucCoA OG IsoCit Cit OAA AcCoA CoAPyr PEP

-METEXT
Sucex Alaex Gluex ADP ATP AMP NH3 Aspex FADH2 FAD NADPH NADP NADH CO2 NAD PG

-CAT
Eno : PG = PEP .
Pyk : PEP + ADP = Pyr + ATP .
AceEF : Pyr + NAD + CoA = AcCoA + CO2 + NADH .
GltA : OAA + AcCoA = Cit + CoA .
Acn : Cit = IsoCit .
Icd : IsoCit + NADP = OG + CO2 + NADPH .
SucAB : OG + NAD + CoA = SucCoA + CO2 + NADH.
SucCD : SucCoA + ADP = Succ + ATP + CoA .
Sdh : Succ + FAD = Fum + FADH2 .
Fum : Fum = Mal .
Mdh : Mal + NAD = OAA + NADH .
Icl : IsoCit = Succ + Gly .
Mas : Gly + AcCoA = Mal + CoA .
AspC : OAA + Glu = Asp + OG .
AspCon : Asp = Aspex .
AspA : Asp = Fum + NH3 .
Gdh : OG + NH3 + NADPH = Glu + NADP .
Pck : OAA + ATP = PEP + ADP + CO2 .
Ppc : PEP + CO2 = OAA .
Pps : Pyr + ATP = PEP + AMP .
GluCon : Glu = Gluex .
IlvEAvtA : Pyr + Glu = Ala + OG .
AlaCon : Ala = Alaex .
SucCoACon : SucCoA = Sucex + CoA
	\end{lstlisting}	
\end{framed}

\newpage

\subsection{Fichier.out}

\begin{framed}
	\begin{lstlisting}
METATOOL OUTPUT Version 3.0 [your path to]\meta3\_int.exeINPUT
FILE: Example.datINTERNAL METABOLITES: 16REACTIONS: 24
STOICHIOMETRIC MATRIX:

matrix dimension 16 x 24
0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0 -1  0
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0 -1 -1  0  0  0  0  0  0
0  0  0  0  0  0 -1  1 -1  0  0  0  0  0  0  0  0  0  0  0  0 -1  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  1 -1  0  0  0  0  0  0  0  0
0  0  0  0  1 -1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0
0  0  0  1 -1  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0
0  0  1 -1  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0
0  0 -1  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0 -1
0  0  0  0  0  0  1 -1  1  0  0  0  1 -1  0  0  0  0  0  0  0  0  0  0
0  1  0  0  0  0  0  0  0  0  0  0 -1  0 -1  0  0  0  0  0  0  0  0  0
0 -1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  1 -1  0  0  0  0 -1  0  0  0  0  0  0 -1  1  0  0  0  0
0  0  0  0  0  0  0  0  0  0  1 -1  0  0  0 -1  0  0  0  0  0  0  0  0
0  0  1  0  0  0  0  0  0  0 -1  1  0 -1  0  1  0  0  0  0  0  0  0  1
0  0  0  0  0  0  0  0 -1  1 -1  0  0  0  0  0  0  0  0  0 -1  0  0  0
1  0  0  0  0  0  0  0  0 -1  0  0  0  0  0  0  0  0  1 -1  1  0  0  0

following line indicates reversible (0) and irreversible reactions
(1) 0  0  0  0  0  0  0  0  0  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1

KERNEL matrix dimension 9 x 24
1  1  1  1  1  1  0  0  0  1  1  1  1  1  0  0  0  0  0  0  0  0  0  0
2  1  0  1  1  2  1  1  0  2  2  1  0  0  1  1  1  0  0  0  0  0  0  0
0  0  0  0  1  1  1  1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0
1  1  0  1  1  2  0  0  0  2  2  1  0  0  1  1  0  0  1  0  0  0  0  0
1  1  0  1  1  2  0  0  0  2  2  1  0  0  1  1  0  0  0 -1  0  0  0  0
0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  1  0  0  0
3  2  0  1  1  2  0  1  0  3  3  2  1  0  1  1  0  0  0  0  0  1  0  0
1  0  0  0  0  0  0  1  1  1  0  0  0  0  0  0  0  0  0  0  0  0  1  0
2  1 -1  0  0  1  0  0  0  2  2  1  0  0  1  1  0  0  0  0  0  0  0  1

enzymes
1: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible
2: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible
3: Fum Mdh AspC Gdh AspA irreversible
4: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible
5: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas -Ppc irreversible
6: Pyk Pps irreversible
7: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible
8: Eno Gdh IlvEAvtA Pyk AlaCon irreversible
9: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible

overall reaction
1: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2
2: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2
3: NADPH + NAD = NADP + NADH 4: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2
5: 2 ADP + FAD + 4 NAD + PG = 2 ATP + FADH2 + 4 NADH + 3 CO2
6: ADP = AMP
7: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2
8: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP
9: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2
	\end{lstlisting}	
\end{framed}

\begin{framed}
	\begin{lstlisting}
SUBSETS of reactions (21 rows) matrix dimension 21 x 24
1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0
0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0
0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  1  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1

enzymes 1: Eno
reversible 2: Acn GltA
irreversible 3: SucCD
reversible 4: Sdh
reversible 5: Fum
reversible 6: Mdh
reversible 7: AspC
reversible 8: Gdh
reversible 9: IlvEAvtA AlaCon
irreversible 10: Pyk
irreversible 11: AceEF
irreversible 12: Icd
irreversible 13: SucAB
irreversible 14: Icl Mas
irreversible 15: AspCon
irreversible 16: AspA
irreversible 17: Pck
irreversible 18: Ppc
irreversible 19: Pps
irreversible 20: GluCon
irreversible 21: SucCoACon irreversible overall reaction

1: PG = PEP
2: OAA + AcCoA = IsoCit + CoA
3: SucCoA + ADP = Succ + CoA + ATP
4: Succ + FAD = Fum + FADH2
5: Fum = Mal
6: Mal + NAD = OAA + NADH
7: Glu + OAA = Asp + OG
8: OG + NH3 + NADPH = Glu + NADP
9: Glu + Pyr = OG + Alaex
10: PEP + ADP = Pyr + ATP
11: CoA + Pyr + NAD = AcCoA + NADH + CO2
12: IsoCit + NADP = OG + NADPH + CO2
13: OG + CoA + NAD = SucCoA + NADH + CO2
14: IsoCit + AcCoA = Mal + Succ + CoA
15: Asp = Aspex
16: Asp = Fum + NH3
17: OAA + ATP = PEP + ADP + CO2
18: PEP + CO2 = OAA
19: Pyr + ATP = PEP + AMP
20: Glu = Gluex
21: SucCoA = CoA + Sucex
	\end{lstlisting}	
\end{framed}

\begin{framed}
	\begin{lstlisting}
REDUCED SYSTEM with 13 branch point
metabolites in 21 reactions (columns) matrix dimension 13 x 21
 0  0  0  0  0  0  1  0  0  0  0  0  0
 0 -1 -1  0  0  0  0 0  0  0  0  0  0
 0 -1  1 -1  0  0  0  0  0  0  0  0  0
 0 -1  0  0  0  0  0  1 -1  0  0  0  0
 0  0  0  1  0  0  0  0  0  0  0  0  0
 0  1 -1  0  0  0  0  0  0  0  0  0  0
 1  0  0  0  0  0  0  0  1 -1  0  0  0
 0  0  0  0  0  0  1  0  0  0  0  0  0
 0  0  0 -1  0  0  0  0  0  0  0  0  0
 1  0  0  0  0  0  0  0 -1  0  0  0  0
 0  0  1 -1  1  0  0  1 -1  0  0  0  0
 0  0  0  0  0  1  0  0  0  0  0  0  0
 0  0 -1  0 -1  0  0  0  0  0  0  0  0
-1  0  0  0  1 -1  0  0  0  0  0  0  0
 0  0 -1  1  0  0  0  0 -1  0  0  0  0
 0  0  0  0  1  0  0 -1  0  0  0  0  0
 0  0  0  1  1  0  0  0  0  0  0  0 -1
 0 -1  1  0  0  0  0  0  0  1  0  0  0
 0  0  0  0  0 -1  1 -1  0  0  0  0  0
 0  0 -1  0  0  1  0  0  0  0  0  0  0
 0 -1  0  0  0  0  0  0  1 -1  1  0  0

following line indicates reversible (0) and irreversible reactions (1)
0  1  0  0  0  0  0  0  1  1  1  1  1  1  1  1  1  1  1  1  1
CONVEX BASIS matrix dimension 12 x 21
0  0  0  0  1  1  1  1  0  0  0  0
0  0  0  1  0  0  0  0  0  0  0  0
0  0  0  0  0  0  0  0  0  0  0  0
0  1  1  0  0  0  0  0  0  0  0  0
0  0  0  1  0  0  0  0  0  0  0  0
1  0  0  1  0  0  0  0  0  1  1  0
0  0  0  0  0  1  0  0  1  0  0  0
1  0 -1 -1 -1 -1  0  0  0  0  0 0
0  0  0  0  0  1  0  0  1  1  0  0
0  0  0  0  1  1  1  0  0  0  0  0
0  0  0  0  0  0  1  1  1  1  1  1
0  0  0  1  1  1  1  0  0  0  0  0
0  0  0  2  1  0  0  0  0  0  1  0
1  1  1  0  0  0  0  0  1  0  1  0
1  1  0  1  1  2  0  0  0  2  2  0
0  1  0  0  1  0  0  0  0  2  1  0
1  1  2  1  1  0  2  2  0  0  1  1
0  0  0  0  0  0  2  1 -1  0  0  1
0  0  0  2  2  0  0  1  0  0  0  0
0  0  1  3  2  0  1  1  2  0  1  0
3  3  1  0  1  0  0  0  0  0  1  0

enzymes
1: Fum Mdh AspC Gdh AspA irreversible
2: Pck Ppc irreversible
3: Pyk Pps irreversible
4: Eno AspC Gdh AspCon Ppc irreversible
5: Eno -SucCD -Sdh -Fum -Mdh Ppc SucCoACon irreversible
6: Eno Gdh IlvEAvtA Pyk AlaCon irreversible
7: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible
8: (2 Eno) Acn Gdh Pyk AceEF GltA Icd Ppc GluCon irreversible
9: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible
10: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible
11: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible
12: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible
	\end{lstlisting}	
\end{framed}
\newpage
\begin{framed}
	\begin{lstlisting}
overall reaction
1: NADPH + NAD = NADP + NADH
2: ATP = ADP
3: ADP = AMP
4: NH3 + NADPH + CO2 + PG = Aspex + NADP
5: ATP + FADH2 + NADH + CO2 + PG = Sucex + ADP + FAD + NAD
6: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP
7: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2
8: ADP + NH3 + NAD + 2 PG = Gluex + ATP + NADH + CO2
9: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2
10: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2
11: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2
12: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2

CONSERVATON RELATIONS
matrix dimension 1 x 16
0  0  0  0  0  0  0  1  0  0  0  0  1  1  0  0

ELEMENTARY MODES

matrix dimension 16 x 21
 0  0  0  0  1  1  1  1  0  0  0  0  0  0  0  1
 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
 0  0  0  0  0  1  1  0  0  0  0  0  0  0  0  0
 0  0  0  1  0  0  0  0  0  0  0  0  1  0  0  1
 0  0  0  0  0  1  1  0  0  0  0  0  0  1  0  0
 1  0  0  0  1  0 -1 -1 -1 -1  0  0  0  0  0  0
 0  0  0  0  0  1  0  0  1  1  0 -1 -1  0  0  1
 1  0  0  0  0  0  0  0  1  0  1  0  0  1  1  0
 0  0  0  0  0  1  1  1  0  0  0  0  0  0  0  0
 0  0  0  2  1 -1  0  0  1  0  0  0  2  2  0  0
 1  0  0  0  0  0  0  1  1  1  1  1  1  1  0  0
 0  1  1  1  1  0  0  0  0  0  0  0  0  3  1 -2
-1 -1  0  0  0  0  2  2  0  0  1  0  0  0  1  0
 0  2  2  1  0  0  0  0  0  1  0  1  1  1  0  0
 0  0  0  1  0  1  0  2  1  0  0  0  0  0  0  0
 1  1  1  1  0  0  0  0  1  0  0  1  1  1  0  1
 1  2  0  0  0  2  2  0  0  1  0  0  1  0  0  0
 0  2  1  0  1  1  2  1  1  0  2  2  0  0  1  1
 0  0  0  0  0  0  3  2  0  1  1  2  0  1  0  3
 3  1  0  1  0  0  0  0  0  1  0  3  2  0  1  1
 2  0  0  0  3  3  1  1  1  0  0  0  0  0  0  1

enzymes
1: Fum Mdh AspC Gdh AspA irreversible
2: Pck Ppc irreversible
3: Pyk Pps irreversible
4: Eno AspC Gdh AspCon Ppc irreversible
5: Eno -SucCD -Sdh -Fum -Mdh Ppc SucCoACon irreversible
6: Eno -SucCD -Sdh AspC Gdh AspA Ppc SucCoACon irreversible
7: Eno Gdh IlvEAvtA Pyk AlaCon irreversible
8: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible
9: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible
10: (3 Eno) Acn (-2 SucCD) -Sdh -Fum (2 Pyk) (2 AceEF) GltA Icl Mas Ppc (2 SucCoACon) irreversible
11: (2 Eno) Acn Gdh Pyk AceEF GltA Icd Ppc GluCon irreversible
12: (2 Eno) Acn Pyk AceEF GltA Icd SucAB Ppc SucCoACon irreversible
13: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible
14: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible
15: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible
16: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) (3 Pyk) (3 AceEF) (2 GltA) Icd SucAB Icl Mas SucCoACon irreversible
	\end{lstlisting}	
\end{framed}
\newpage
\begin{framed}
	\begin{lstlisting}
overall reaction
1: NADPH + NAD = NADP + NADH
2: ATP = ADP
3: ADP = AMP
4: NH3 + NADPH + CO2 + PG = Aspex + NADP
5: ATP + FADH2 + NADH + CO2 + PG = Sucex + ADP + FAD + NAD
6: ATP + FADH2 + NADPH + CO2 + PG = Sucex + ADP + FAD + NADP
7: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP
8: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2
9: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2
10: FADH2 + 2 NAD + 3 PG = 2 Sucex + FAD + 2 NADH + CO2
11: ADP + NH3 + NAD + 2 PG = Gluex + ATP + NADH + CO2
12: ADP + NADP + 2 NAD + 2 PG = Sucex + ATP + NADPH + 2 NADH + 2 CO2
13: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2
14: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2
15: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2
16: 3 ADP + FAD + NADP + 6 NAD + 3 PG = Sucex + 3 ATP + FADH2 + NADPH + 6 NADH + 5 CO2

The elementary modes 6 10 12 16 are additional to the convex basis.
	\end{lstlisting}	
\end{framed}



%%%% Insertion pdf

